The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity

AbstractBiogenesis of eukaryotic box C/D small nucleolar ribonucleoproteins initiates co-transcriptionally and requires the action of the assembly machinery including the Hsp90/R2TP complex, the Rsa1p:Hit1p heterodimer and the Bcd1 protein. We present genetic interactions between the Rsa1p-encoding gene and genes involved in chromatin organization including RTT106 that codes for the H3-H4 histone chaperone Rtt106p controlling H3K56ac deposition. We show that Bcd1p binds Rtt106p and controls its transcription-dependent recruitment by reducing its association with RNA polymerase II, modulating H3K56ac levels at gene body. We reveal the 3D structures of the free and Rtt106p-bound forms of Bcd1p using nuclear magnetic resonance and X-ray crystallography. The interaction is also studied by a combination of biophysical and proteomic techniques. Bcd1p interacts with a region that is distinct from the interaction interface between the histone chaperone and histone H3. Our results are evidence for a protein interaction interface for Rtt106p that controls its transcription-associated activity.

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Chaperone Control of the Activity and Specificity of the Histone H3 Acetyltransferase Rtt109

Molecular and Cellular Biology ◽

10.1128/mcb.00182-08 ◽

2008 ◽

Vol 28 (13) ◽

pp. 4342-4353 ◽

Cited By ~ 130

Author(s):

Jeffrey Fillingham ◽

Judith Recht ◽

Andrea C. Silva ◽

Bernhard Suter ◽

Andrew Emili ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Histone Acetyltransferase ◽

Histone H3 ◽

Histone Chaperone ◽

Genetic Interactions ◽

Whole Genome ◽

Genome Screen ◽

Associated Lesions

ABSTRACT Acetylation of Saccharomyces cerevisiae histone H3 on K56 by the histone acetyltransferase (HAT) Rtt109 is important for repairing replication-associated lesions. Rtt109 purifies from yeast in complex with the histone chaperone Vps75, which stabilizes the HAT in vivo. A whole-genome screen to identify genes whose deletions have synthetic genetic interactions with rtt109Δ suggests Rtt109 has functions in addition to DNA repair. We show that in addition to its known H3-K56 acetylation activity, Rtt109 is also an H3-K9 HAT, and we show that Rtt109 and Gcn5 are the only H3-K9 HATs in vivo. Rtt109's H3-K9 acetylation activity in vitro is enhanced strongly by Vps75. Another histone chaperone, Asf1, and Vps75 are both required for acetylation of lysine 9 on H3 (H3-K9ac) in vivo by Rtt109, whereas H3-K56ac in vivo requires only Asf1. Asf1 also physically interacts with the nuclear Hat1/Hat2/Hif1 complex that acetylates H4-K5 and H4-K12. We suggest Asf1 is capable of assembling into chromatin H3-H4 dimers diacetylated on both H4-K5/12 and H3-K9/56.

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Integrative structural Investigation on the architecture of human Importin4_histone H3/H4_Asf1a complex and its histone H3 tail binding

10.1101/181321 ◽

2017 ◽

Author(s):

Jungmin Yoon ◽

Seung Joong Kim ◽

Sojin An ◽

Alexander Leitner ◽

Taeyang Jung ◽

...

Keyword(s):

Histone H3 ◽

Terminal Region ◽

Nuclear Localization Sequence ◽

Molecular Architecture ◽

X Ray ◽

X Ray Crystallography ◽

Integrative Modeling ◽

Negative Stain ◽

Localization Sequence ◽

Chaperone Complex

AbstractImportin4 transports histone H3/H4 in complex with Asf1a to the nucleus for chromatin assembly. Importin4 recognizes the nuclear localization sequence located at the N-terminal tail of histones. Here, we analyzed the structures and interactions of human Importin4, histones and Asf1a by cross-linking mass spectrometry, X-ray crystallography, negative-stain electron microscopy, small-angle X-ray scattering and integrative modeling. The XL-MS data showed that the C-terminal region of Importin4 interacts extensively with the histone H3 tail. We determined the crystal structure of the C-terminal region of Importin4 bound to the histone H3 peptide, thus revealing that the acidic path in Importin4 accommodates the histone H3 tail and that histone H3 Lys14 is the primary residue interacting with Importin4. Furthermore, the molecular architecture of the Importin4_histone H3/H4_Asf1a complex was produced through an integrative modeling approach. Overall, this work provides structural insights into how Importin4 recognizes histones and their chaperone complex.

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Crystal structure of bacterial succinate:quinone oxidoreductase flavoprotein SdhA in complex with its assembly factor SdhE

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1800195115 ◽

2018 ◽

Vol 115 (12) ◽

pp. 2982-2987 ◽

Cited By ~ 9

Author(s):

Megan J. Maher ◽

Anuradha S. Herath ◽

Saumya R. Udagedara ◽

David A. Dougan ◽

Kaye N. Truscott

Keyword(s):

Succinate Dehydrogenase ◽

Flavin Adenine Dinucleotide ◽

Tricarboxylic Acid Cycle ◽

Direct Interaction ◽

X Ray ◽

X Ray Crystallography ◽

Open Conformation ◽

Transport Chain ◽

Assembly Factor ◽

Succinate:Quinone Oxidoreductase

Succinate:quinone oxidoreductase (SQR) functions in energy metabolism, coupling the tricarboxylic acid cycle and electron transport chain in bacteria and mitochondria. The biogenesis of flavinylated SdhA, the catalytic subunit of SQR, is assisted by a highly conserved assembly factor termed SdhE in bacteria via an unknown mechanism. By using X-ray crystallography, we have solved the structure of Escherichia coli SdhE in complex with SdhA to 2.15-Å resolution. Our structure shows that SdhE makes a direct interaction with the flavin adenine dinucleotide-linked residue His45 in SdhA and maintains the capping domain of SdhA in an “open” conformation. This displaces the catalytic residues of the succinate dehydrogenase active site by as much as 9.0 Å compared with SdhA in the assembled SQR complex. These data suggest that bacterial SdhE proteins, and their mitochondrial homologs, are assembly chaperones that constrain the conformation of SdhA to facilitate efficient flavinylation while regulating succinate dehydrogenase activity for productive biogenesis of SQR.

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Structural insights into histone chaperone Asf1 and its characterization from Plasmodium falciparum

Biochemical Journal ◽

10.1042/bcj20200891 ◽

2021 ◽

Author(s):

Dushyant Kumar Srivastava ◽

Sarika Gunjan ◽

Chandrima Das ◽

Vasudevan Seshadri ◽

Siddhartha Roy

Keyword(s):

Plasmodium Falciparum ◽

Histone H3 ◽

Histone Chaperone ◽

Site Directed Mutagenesis ◽

Nucleosome Assembly ◽

Significant Similarity ◽

X Ray Crystallography ◽

Dimerization Interface ◽

Tightly Coupled ◽

Dna Template

Asf1 is a highly-conserved histone chaperone that regulates tightly-coupled nucleosome assembly/disassembly process. We observed that Plasmodium falciparum Asf1 (PfAsf1) is ubiquitously expressed in different stages of the life cycle of the parasite. To gain further insight into its biological activity, we solved the structure of N-terminal histone chaperone domain of PfAsf1(1-159 amino acids) by X-ray crystallography to a resolution of 2.4 Å. The structure is composed of two beta-sheet to form a beta-sandwich, which resembles an immunoglobulin-like fold. The surface-charge distribution of PfAsf1 is distinct from yAsf1 and hAsf1 although the core-structure shows significant similarity. The crystal-structure indicated that PfAsf1 may exist in a dimeric-state which was further confirmed by solution cross-linking experiment. PfAsf1 was found to specifically interact with Plasmodium histone H3 and H4 and was able to deposit H3/H4 dimer onto DNA-template to form disomes, showing its characteristic histone chaperone activity. We mapped the critical residues of PfAsf1 involved in histone H3/H4 interaction and confirmed by site directed mutagenesis. Further analysis indicates that histone interacting surface of Asf1 is highly conserved while the dimerization interface is variable. Our results identify the role of PfAsf1 as mediator of chromatin assembly in Plasmodium falciparum, which is the causative agent of malignant malaria in humans.

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The Histone Chaperone TAF-I/SET/INHAT Is Required for Transcription In Vitro of Chromatin Templates

Molecular and Cellular Biology ◽

10.1128/mcb.25.2.797-807.2005 ◽

2005 ◽

Vol 25 (2) ◽

pp. 797-807 ◽

Cited By ~ 44

Author(s):

Matthew J. Gamble ◽

Hediye Erdjument-Bromage ◽

Paul Tempst ◽

Leonard P. Freedman ◽

Robert P. Fisher

Keyword(s):

Rna Polymerase Ii ◽

Transcriptional Activation ◽

Nuclear Extract ◽

Histone Chaperone ◽

Chromatin Assembly ◽

Polymerization Reaction ◽

Naked Dna ◽

Assembly Factor ◽

Transcript Elongation

ABSTRACT To uncover factors required for transcription by RNA polymerase II on chromatin, we fractionated a mammalian cell nuclear extract. We identified the histone chaperone TAF-I (also known as INHAT [inhibitor of histone acetyltransferase]), which was previously proposed to repress transcription, as a potent activator of chromatin transcription responsive to the vitamin D3 receptor or to Gal4-VP16. TAF-I associates with chromatin in vitro and can substitute for the related protein NAP-1 in assembling chromatin onto cloned DNA templates in cooperation with the remodeling enzyme ATP-dependent chromatin assembly factor (ACF). The chromatin assembly and transcriptional activation functions are distinct, however, and can be dissociated temporally. Efficient transcription of chromatin assembled with TAF-I still requires the presence of TAF-I during the polymerization reaction. Conversely, TAF-I cannot stimulate transcript elongation when added after the other factors necessary for assembly of a preinitiation complex on naked DNA. Thus, TAF-I is required to facilitate transcription at a step after chromatin assembly but before transcript elongation.

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Difference Fourier Analysis of Glucose Embedded and Frozen Hydrated Purple Membrane

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100053164 ◽

1982 ◽

Vol 40 ◽

pp. 74-75

Author(s):

Jules S. Jaffe ◽

Robert M. Glaeser

Keyword(s):

Purple Membrane ◽

Data Set ◽

High Resolution Data ◽

X Ray ◽

X Ray Crystallography ◽

Fourier Techniques ◽

Versus Protein ◽

The Difference ◽

Difference Fourier ◽

Ideal Method

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.

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3-D reconstruction of molecular shape from microcrystal thin sections

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100077311 ◽

1983 ◽

Vol 41 ◽

pp. 748-749

Author(s):

S. Cusack ◽

J.-C. Jésior

Keyword(s):

Three Dimensional ◽

Molecular Shape ◽

Biological Molecules ◽

Fourier Space ◽

Single Particles ◽

Thin Sections ◽

Standard Methods ◽

X Ray ◽

X Ray Crystallography ◽

Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

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Electron microscopy of rabbit FC crystals

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100077220 ◽

1983 ◽

Vol 41 ◽

pp. 730-731

Author(s):

Robert A. Grant ◽

Laura L. Degn ◽

Wah Chiu ◽

John Robinson

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

High Resolution Electron Microscopy ◽

Molecular Replacement ◽

X Ray ◽

X Ray Crystallography ◽

Resolution Electron ◽

Replacement Technique ◽

Hydrated Crystal ◽

Molecular Structure Analysis

Proteolytic digestion of the immunoglobulin IgG with papain cleaves the molecule into an antigen binding fragment, Fab, and a compliment binding fragment, Fc. Structures of intact immunoglobulin, Fab and Fc from various sources have been solved by X-ray crystallography. Rabbit Fc can be crystallized as thin platelets suitable for high resolution electron microscopy. The structure of rabbit Fc can be expected to be similar to the known structure of human Fc, making it an ideal specimen for comparing the X-ray and electron crystallographic techniques and for the application of the molecular replacement technique to electron crystallography. Thin protein crystals embedded in ice diffract to high resolution. A low resolution image of a frozen, hydrated crystal can be expected to have a better contrast than a glucose embedded crystal due to the larger density difference between protein and ice compared to protein and glucose. For these reasons we are using an ice embedding technique to prepare the rabbit Fc crystals for molecular structure analysis by electron microscopy.

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